7VC3

Toxoplasma gondii Prolyl-tRNA Synthetase (TgPRS) in Complex with inhibitor L97 and L-proline at 1.97 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7F9T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M Amino acids (0.2M DL-Glutamic acid monohydrate, 0.2M DL-Alanine, 0.2M Glycine, 0.2M DL-Lysine monohydrochloride and 0.2M DL-Serine) 0.1 M Buffer (Sodium HEPES, MOPS), 30 % v/v Precipitant (40% v/v Glycerol, 20% w/v PEG 4000)
Crystal Properties
Matthews coefficientSolvent content
2.5451.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.733α = 90
b = 73.644β = 111.38
c = 74.906γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2019-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.9760.6498.6110.76.940410
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.972.0197.90.40.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7F9T1.97352.6821.3439532198196.450.1770.17480.217454.3235
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3906
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms81

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing